I've played around with this a bit to see what happens.
You get to the part which looks like Port Royale dungeon through the back door to the Maltese Abbey in Bridgetown. One of the passages which is a dead end in Port Royale leads from the Bridgetown version to the temple.
There is no screaming and message in the middle of the church. After wiping out all the monks so that I could wander around without being disturbed, I walked up and down the length of the blue carpet along the whole middle of the church, round the altar, several times, and did not scream once. The only place where anything happened was the trapdoor near the wall. This dropped me into the crypt.
Where I did have a similar experience was in the crypt itself, so I saved game, changed "InternalSettings.h" to make locators visible, then loaded the game to see which locator was causing the trouble. It's supposed to send you to that dungeon which looks like the one in Port Royale. So I loaded another savegame in which I'm outside the Maltese Abbey, went round the back and into the dungeon, found my way from there to the crypt, and was indeed back where I'd had the scream, the message about a trapdoor, but no teleport to the dungeon. This time, when I moved away and went back to the locator, it did send me to the dungeon.
The problem is probably this, in the definition of the crypt:
Code:
Locations[n].reload.l3.name = "reload12"; // circle to reload25
Locations[n].reload.l3.go = "Greenford_M_crypt"; // KK
Locations[n].reload.l3.emerge = "Reload25";
Locations[n].reload.l3.autoreload = "1";
Locations[n].reload.l8.name = "reload25"; // circle to reload12
Locations[n].reload.l8.go = "Greenford_M_crypt"; // KK
Locations[n].reload.l8.emerge = "reload12";
Locations[n].reload.l8.autoreload = "1";
What that does is send you from one part of the crypt to another part of the same crypt. This sort of loop has caused trouble before, in the jungle on Antigua, which was fixed by making a new location and linking both exits from the troublesome area to that new location. In the real Cozumel temple, "reload12" and "reload25" link to another part of the labyrinth. So to fix this one, someone would need to define a new location, possibly another level of the crypt, and then link "reload12" and "reload25" to there.